rs11230550

Positions:

• chr11-60984534-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006725.5(CD6):​c.49+12620G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0932 in 152,272 control chromosomes in the GnomAD database, including 764 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.093 (764 hom., cov: 32)
• Consequence: CD6 NM_006725.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

CD6 (HGNC:1691): (CD6 molecule) This gene encodes a protein found on the outer membrane of T-lymphocytes as well as some other immune cells. The encoded protein contains three scavenger receptor cysteine-rich (SRCR) domains and a binding site for an activated leukocyte cell adhesion molecule. The gene product is important for continuation of T cell activation. This gene may be associated with susceptibility to multiple sclerosis (PMID: 19525953, 21849685). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD6	NM_006725.5	c.49+12620G>A		intron_variant		ENST00000313421.11	NP_006716.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD6	ENST00000313421.11	c.49+12620G>A		intron_variant		1	NM_006725.5	ENSP00000323280.7

Frequencies

GnomAD3 genomes AF: 0.0932 AC: 14184 AN: 152154 Hom.: 764 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0661

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0856

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0932 AC: 14194 AN: 152272 Hom.: 764 Cov.: 32 AF XY: 0.0921 AC XY: 6853 AN XY: 74448

Gnomad4 AFR AF: 0.0697

Gnomad4 AMR AF: 0.0659

Gnomad4 ASJ AF: 0.0855

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0248

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.0848

Alfa AF: 0.103 Hom.: 328

Bravo AF: 0.0898

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11230550; hg19: chr11-60752006;